Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins

N Vakirlis, A Kupczok - Genome Research, 2024 - genome.cshlp.org
Species-specific genes, also known as orphans, are ubiquitous across life's domains. In
prokaryotes, species-specific orphan genes (SSOGs) are mostly thought to originate in …

Persistent, Private, and Mobile Genes: A Model for Gene Dynamics in Evolving Pangenomes

J Gamblin, A Lambert, F Blanquart - Molecular Biology and …, 2025 - academic.oup.com
The pangenome of a species is the set of all genes carried by at least one member of the
species. In bacteria, pangenomes can be much larger than the set of genes carried by a …

Evolutionary dynamics of the accessory genomes of Staphylococcus aureus

KR Piper, OO Ikhimiukor, SSR Souza, T Garcia-Aroca… - Msphere, 2024 - Am Soc Microbiol
Staphylococcus aureus is a ubiquitous commensal and opportunistic bacterial pathogen that
can cause a wide gamut of infections, which are exacerbated by the presence of multidrug …

A universal and constant rate of gene content change traces pangenome flux to LUCA

K Trost, MR Knopp, JLE Wimmer… - FEMS microbiology …, 2024 - academic.oup.com
Prokaryotic genomes constantly undergo gene flux via lateral gene transfer, generating a
pangenome structure consisting of a conserved core genome surrounded by a more …

Pangenomes reveal genomic signatures of microbial adaptation to experimental soil warming

MJ Choudoir, A Narayanan, D Rodriguez-Ramos… - bioRxiv, 2023 - biorxiv.org
Below-ground carbon transformations represent a natural climate change mitigation
solution, but newly-acquired traits adaptive to climate stress may alter microbial climate …

Large-scale investigation of orphan genes in the human gut microbiome elucidates their evolutionary origins

N Vakirlis, A Kupczok - bioRxiv, 2023 - biorxiv.org
Orphan genes, ie, genes that lack homologs outside a given species, are ubiquitous in all
domains of life. In prokaryotes, orphans can originate (i) in the native genome via de novo …

A simple path to complexity: horizontal gene transfer in microbial communities

P Buffard - 2023 - macau.uni-kiel.de
In nature, microbial communities are inherent components of all ecosystems, actively
sha** and being shaped by complex eco-evolutionary feedback processes. Importantly …